Integrated imaging instrument for self-calibrated fluorescence protein microarrays.

Protein microarrays, or multiplexed and high-throughput assays, monitor multiple protein binding events to facilitate the understanding of disease progression and cell physiology. Fluorescence imaging is a popular method to detect proteins captured by immobilized probes with high sensitivity and specificity. Reliability of fluorescence assays depends on achieving minimal inter- and intra-assay probe immobilization variation, an ongoing challenge for protein microarrays. Therefore, it is desirable to establish a label-free method to quantify the probe density prior to target incubation to calibrate the fluorescence readout. Previously, a silicon oxide on silicon chip design was introduced to enhance the fluorescence signal and enable interferometric imaging to self-calibrate the signal with the immobilized probe density. In this paper, an integrated interferometric reflectance imaging sensor and wide-field fluorescence instrument is introduced for sensitive and calibrated microarray measurements. This platform is able to analyze a 2.5 mm × 3.4 mm area, or 200 spots (100 µm diameter with 200 µm pitch), in a single field-of-view.

Synergetic chemiluminescence and label-free dual detection for developing a hepatitis protein array.

A dual detection system for protein arrays is presented that combines label-free detection by optical interference with chemiluminescence. A planar protein array that targets hepatitis B surface antigen is developed. Surface densities for individual antibody spots are quantitated using optical interference prior to use. Target binding (10 ng/ml) is detected label-free. Target binding (1 ng/ml) is detected by both optical interference and chemiluminescence with the inclusion of secondary antibodies. Binding results using both methods are found to be directly proportion to the capture probe density measured initially. The dual detection system provides the analytical utility of optical interference detection with the established clinical utility of chemiluminescence detection.

LED-based interferometric reflectance imaging sensor for quantitative dynamic monitoring of biomolecular interactions.

Label-free optical biosensors have been established as proven tools for monitoring specific biomolecular interactions. However, compact and robust embodiments of such instruments have yet to be introduced in order to provide sensitive, quantitative, and high-throughput biosensing for low-cost research and clinical applications. Here we present the Interferometric Reflectance Imaging Sensor (IRIS) using an inexpensive and durable multi-color LED illumination source to monitor protein-protein and DNA-DNA interactions. We demonstrate the capability of this system to dynamically monitor antigen-antibody interactions with a noise floor of 5.2 pg/mm(2) and DNA single mismatch detection under denaturing conditions in an array format. Our experiments show that this platform has comparable sensitivity to high-end label-free biosensors at a much lower cost with the capability to be translated to field-deployable applications.

Multiplexed, rapid point of care platform to quantify allergen-specific IgE.

Variation of probe immobilization on microarrays hinders the ability to make high quality, assertive and statistically relevant conclusions needed in the healthcare setting. To address this problem, we have developed a calibrated, compact, inexpensive, multiplexed, dual modality point-of-care detection platform that calibrates and correlates surface probe density measured label-free to captured labeled secondary antibody, is independent of chip-to-chip variability, and improves upon existing diagnostic technology. We have identified four major technological advantages of our proposed platform: the capability to perform single spot analysis based on the fluorophore used for detection, a 10-fold gain in fluorescence signal due to optimized substrate, a calibrated, quantitative method that uses the combined fluorescent and label-free modalities to accurately measure the density of probe and bound target for a variety of systems, and a compact measurement platform offering reliable and rapid results at the doctor's office. Already, we have formulated over a 90% linear correlation between the amount of probe bound to surface and the resulting fluorescence of captured target for IgG, ß-lactoglobulin, Ara h 1 peanut allergen, and Phl 5a Timothy grass allergen.

High-throughput detection and sizing of individual low-index nanoparticles and viruses for pathogen identification.

Rapid, chip-scale, and cost-effective single particle detection of biological agents is of great importance to human health and national security. We report real-time, high-throughput detection and sizing of individual, low-index polystyrene nanoparticles and H1N1 virus. Our widefield, common path interferometer detects nanoparticles and viruses over a very large sensing area, orders of magnitude larger than competing techniques. We demonstrate nanoparticle detection and sizing down to 70 nm in diameter. We clearly size discriminate nanoparticles with diameters of 70, 100, 150, and 200 nm. We also demonstrate detection and size characterization of hundreds of individual H1N1 viruses in a single experiment.

Subsurface microscopy of integrated circuits with angular spectrum and polarization control.

We investigate the effect of an annular pupil-plane aperture in confocal imaging while using an NA increasing lens. We show that focal spot shape is highly sensitive to both polarization and angular spectrum of the incoming light. We demonstrate a lateral spatial resolution of 145 nm (lambda(0)/9) in the direction perpendicular to the polarization direction.

Strong extinction of a far-field laser beam by a single quantum dot.

Through the utilization of index-matched GaAs immersion lens techniques, we demonstrate a record extinction (12%) of a far-field focused laser beam by a single InAs/GaAs quantum dot. This contrast level enables us to report for the first time resonant laser transmission spectroscopy on a single InAs/GaAs quantum dot without the need for phase-sensitive lock-in detection.

Optical determination of electron-phonon coupling in carbon nanotubes.

We report on an optical method to directly measure electron-phonon coupling in carbon nanotubes by correlating the first and second harmonic of the resonant Raman excitation profile. The method is applicable to 1D and 0D systems and is not limited to materials that exhibit photoluminescence. Experimental results for electron-phonon coupling with the radial breathing mode in 5 different nanotubes show coupling strengths from 3-11 meV. The results are in good agreement with the chirality and diameter dependence of the e-ph coupling calculated by Goupalov et al.

Phase-sensitive detection of dipole radiation in a fiber-based high numerical aperture optical system.

We theoretically study the problem of detecting dipole radiation in a fiber-based confocal microscope of high numerical aperture. By using a single-mode fiber, in contrast to a hard-stop pinhole aperture, the detector becomes sensitive to the phase of the field amplitude. We find that the maximum in collection efficiency of the dipole radiation does not coincide with the optimum resolution for the light-gathering instrument. The derived expressions are important for analyzing fiber-based confocal microscope performance in fluorescence and spectroscopic studies of single molecules and/or quantum dots.

Temperature dependence of the optical transition energies of carbon nanotubes: the role of electron-phonon coupling and thermal expansion.

Tunable Raman spectroscopy is used to measure the optical transition energies Eii of individual single wall carbon nanotubes. Eii is observed to shift down in energy by as much as 50 meV, from -160 to 300 degrees C, in contrast with previous measurements performed on nanotubes in alternate environments, which show upshifts and downshifts in Eii with temperature. We determine that electron-phonon coupling explains our experimental observations of nanotubes suspended in air, neglecting thermal expansion. In contrast, for nanotubes in surfactant or in bundles, thermal expansion of the nanotubes' environment exerts a nonisotropic pressure on the nanotube that dominates over the effect of electron-phonon coupling.

Resonance Raman spectroscopy characterization of single-wall carbon nanotube separation by their metallicity and diameter.

Several techniques were recently reported for the bulk separation of metallic (M) and semiconducting (S) single wall carbon nanotubes (SWNTs), using optical absorption and resonance Raman spectroscopy (RRS) as a proof of the separation. In the present work, we develop a method for the quantitative evaluation of the M to S separation ratio, and also for the SWNT diameter selectivity of the separation process, based on RRS. The relative changes in the integrated intensities of the radial-breathing mode (RBM) features, with respect to the starting material, yield the diameter probability distribution functions for M and S SWNTs in the separated fractions, accounting for the different resonance conditions of individual SWNTs, while the diameter distribution of the starting material is obtained following the fitting procedure developed by Kuzmany and coworkers. Features other than the RBM are generally less effective for characterization of the separation process for SWNTs.

Measuring the uniaxial strain of individual single-wall carbon nanotubes: resonance Raman spectra of atomic-force-microscope modified single-wall nanotubes.

Raman spectroscopy is used to measure the strain in individual single-wall carbon nanotubes, strained by manipulation with an atomic-force-microscope tip. Under strains varying from 0.06%-1.65%, the in-plane vibrational mode frequencies are lowered by as much as 1.5% (40 cm(-1)), while the radial breathing mode (RBM) remains unchanged. The RBM Stokes/anti-Stokes intensity ratio remains unchanged under strain. The elasticity of these strain deformations is demonstrated as the down-shifted Raman modes resume their prestrain frequencies after a nanotube is broken under excessive strain.

Resonance Raman spectra of carbon nanotubes by cross-polarized light.

Resonance Raman studies on single wall carbon nanotubes (SWNTs) show that resonance with cross polarized light, i.e., with the E(mu,mu+/-1) van Hove singularities in the joint density of states needs to be taken into account when analyzing the Raman and optical absorption spectra from isolated SWNTs. This study is performed by analyzing the polarization, laser energy, and diameter dependence of two Raman features, the tangential modes (G band) and a second-order mode (G' band), at the isolated SWNT level.

Influence of hot-carrier luminescence from avalanche photodiodes on time-correlated photon detection.

We present the results of our time-resolved measurements of hot-carrier luminescence from passively quenched Geiger-mode avalanche photodiodes. In time-correlated photon-counting (TCPC) experiments, hot-carrier luminescence interferes overwhelmingly with the coincidence spectrum, which results in artifacts. This potential problem should be taken into account in setting up TCPC experiments.